The Relationship of Structure to the Effectiveness of Denaturing Agents for Deoxyribonucleic Acid

Levine, Lawrence; Gordon, Julius A.; Jencks, William P.

doi:10.1021/bi00901a030

Cited by 190 publications

(90 citation statements)

References 22 publications

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“…By using the analytical ultracentrifuge, DNA has been found to be dehydrated upon increase of temperature (4)(5)(6). It has been reported that DNA denaturation occurs in a number of organic solvents due to dehydration (7)(8)(9)(10)(11). Extensive studies of the effect of dehydration on DNA conformation have been carried out using circular dichroism (CD).…”

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confidence: 99%

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Unwinding of double-stranded DNA helix by dehydration.

Lee¹,

Mizusawa²,

Kakefuda³

1981

Proc. Natl. Acad. Sci. U.S.A.

152

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Conformational changes of the double-stranded DNA helix in response to dehydration were investigated by monitoring, by agarose gel electrophoresis, the linking number of covalently closed circular DNA generated by ligation of linear DNA in the presence of different organic solvents or at different temperatures. It was found that: (i) The Hydration and dehydration of DNA has been studied for the past two decades (see refs. 1-3 for reviews). By using the analytical ultracentrifuge, DNA has been found to be dehydrated upon increase of temperature (4-6). It has been reported that DNA denaturation occurs in a number of organic solvents due to dehydration (7-11). Extensive studies of the effect of dehydration on DNA conformation have been carried out using circular dichroism (CD). The conformation of DNA in a thin film (12) or in aqueous organic solvent mixtures (13-18) has been correlated to the spectral change of CD. The decrease of the CD band at 270 nm in the presence of organic solvent has been attributed to the presence ofC form DNA (C DNA) (12-18). On this basis, C DNA has been assumed to prevail at high salt concentrations (19)(20)(21)(22)(23)(24) or under low temperature conditions (in the premelting region) (25,26). However, the presence of C DNA is not supported by x-ray diffraction studies of the DNA in concentrated salt solutions (27) or in organic solvent/water mixtures (27, 28). DNA condensed from various ethanol/water solutions also failed to show the x-ray diffraction pattern of the C form (29).Although a considerable amount of data has been accumulated, no conclusive results have been published to relate hydration of the DNA to its helical structure in solution. Depew and Wang (30) and Pulleyblank et al. (31) showed that the thermal effect on the DNA base-pair twisting angle could be accurately determined by agarose gel electrophoresis of covalently closed circular DNA generated at different temperatures. This type of system is useful for studying DNA structure in solution. For example, using a gel electrophoresis technique, Wang (32,33) demonstrated that the DNA double helix has 10.4 ± 0.1 base pairs per helical turn in dilute solution. [It should be pointed out that Zimmerman and Pheiffer (34) found 9.9 base pairs per turn for DNA in concentrated solution. ] In the present studies, we have explored the effect of hydration on the helical structure of DNA in solution, using phage T4 DNA ligase to covalently close the linear plasmid DNA (pBR322 and pNT7) at various levels of dehydration by addition of methanol, ethanol, glycerol, ethylene glycol, dimethyl sulfoxide, and tetrahydrofuran or exposure to different temperatures. The thermodynamic properties of superhelix formation and the conformational changes of DNA resulting from the different states of dehydration are discussed. An argument is made for the interpretation of the CD spectra of DNA in organic solvent/water mixtures and those in the premelting temperature regions. The implications of DNA hydration and dehydration and their effec...

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confidence: 99%

“…More hydrophobic organic solvents such as tetrahydrofuran (data not shown because of difficulty ofcontrolling the concentration in the experiment due to its volatility) exhibit a similar effect. Thus, such unwinding of the DNA duplex caused by dehydration is likely to be a common phenomenon in organic solvents (10). Two-Dimensional Gel Electrophoresis.…”

mentioning

confidence: 99%

Unwinding of double-stranded DNA helix by dehydration.

Lee¹,

Mizusawa²,

Kakefuda³

1981

Proc. Natl. Acad. Sci. U.S.A.

152

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“…The 4-5 M-DMSO solution remained transparent and pink, while the 1-5 M-DMSO solution was opaque and white. The 30 M-DMSO solution was intermediate between (Levine et al, 1963), and RNA (Crawford et al, 1971), and denatured RNA will reaggregate when the DMSO is removed (Birnboim, 1972). DMSO can also transform cell lines (Ashwood-Smith, 1985), and destabilize proteins (Fahy, 1989 (Herskovits & Harrington, 1972 (Fahy, 1989).…”

Section: Chromosomal Analysismentioning

confidence: 99%

An association between chromosomal abnormalities in rapidly frozen 2-cell mouse embryos and the ice-forming properties of the cryoprotective solution

Shaw

Kola

MacFarlane³

et al. 1991

Reproduction

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Summary. This paper investigates the effect of straw handling on the viability of 2-cell mouse embryos rapidly frozen in dimethyl sulphoxide (DMSO) solutions. During the brief (3 min) equilibration step, straws were either rotated periodically to keep the embryos in suspension, or kept still to allow the embryos to settle onto the inner surface of the straw. The effects of these straw movements were tested with cryoprotectant solutions containing 1\m=.\5,3\m=.\0 or 4\m=.\5m-DMSO. Rapidly cooled straws containing 4\m=.\5m\ x=r eq-\ DMSO vitrify throughout on cooling, but ice forms on warming. The survival and normality of embryos frozen in 4\m=.\5m-DMSO was not influenced by straw handling as 91\p=n-\92%formed blastocysts in vitro, 77\p=n-\78%formed normal fetuses, and no chromosomal rearrangements were observed. In solutions containing < m-DMSO ice formation occurred throughout (1\m=.\5m-DMSO), or in parts (3\m=.\0m-DMSO) of the cryoprotectant during cooling. The viability of embryos frozen in 3\ m=. \ 0 or 1\m=.\5m-DMSO solutions was reduced both in vitro and in vivo and structural chromosome aberrations, predominantly tri-and quadri-radial rearrangements, were observed. The reduction in embryo viability, and the chromosomal damage was particularly pronounced in embryos frozen in 3\ m=. \ 0 m-DMSO in straws which were rotated during the equilibration step (47% blastocysts, 15% fetuses, 77% chromosome rearrangements). The results indicate that rapid freezing of 2-cell mouse embryos in 4\m=.\5 m-DMSO is safe and efficient, whereas freezing at lower DMSO concentrations is associated with severe chromosome damage, and reduced viability in vitro and in vivo.

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“…Urea is a non-electrolyte and hydrophilic water structure breaker (Whitney and Tanford, 1962;Levine et al, 1963;Palma and Morel, 1981), physiologically important compound and has a wide range of bioinorganic (Wages et al, 1993;Koga et al, 1998) and pharmaceutical (Stetsenko et al, 1978;Theophanides and Harvey, 1987) applications. Pt -urea complexes have antitumor activity (Stetsenko et al, 1978).…”

Section: Introductionmentioning

confidence: 99%

Effect of urea on speciation of cobalt(II) complexes of L-glutamine and succinic acid

Ramakrishna

Rao

2007

Chemical Speciation & Bioavailability

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Speciation of CoII complexes of L-glutamine (Gln) and succinic acid (Suc) in 0.0 -36.83%, wyv ureawater mixtures at an ionic strength of 0.16 mol dm À3 and temperature 303.0 AE 0.1 K has been investigated pH-metrically. The species detected for Gln complexes are ML, MLH and ML 3 H and those for Suc are ML, MLH and ML 2 H. The stability of the complexes decreased with increased urea content due to the electrostatic forces, denaturing power and complexing ability of urea. The relative stabilities of the species in urea -water and ethylene glycol -water mixtures are compared based on the dielectric constants. The species distribution and the plausible equilibria for the formation of the species are also presented.

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The Relationship of Structure to the Effectiveness of Denaturing Agents for Deoxyribonucleic Acid

Cited by 190 publications

References 22 publications

Unwinding of double-stranded DNA helix by dehydration.

Unwinding of double-stranded DNA helix by dehydration.

An association between chromosomal abnormalities in rapidly frozen 2-cell mouse embryos and the ice-forming properties of the cryoprotective solution

Effect of urea on speciation of cobalt(II) complexes of L-glutamine and succinic acid

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